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I am using Looper. While running looper run project_config.yaml I am getting duplicate sample name error. I have two fastq files for each sample, so in the annotation.csv file I have:

sample_name,library,file
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r1.fq.gz
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r2.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r1.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r2.fq.gz

My pipeline_interface.yaml file looks the following way:

protocol_mapping:
  RNA-seq: sandro_rna_seq

pipelines:
  sandro_rna_seq:
    name: sandro_rna_seq
    path: sandro_rna_seq.py  # relative to this 
pipeline_interface.yaml file
    looper_args: True
    arguments:
      "-L": "IU"
      "-T": "gencode_mouse_m13"
      "-E": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/jyvo_experiment-metadata.yaml"
      "-C": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/salmon_rna_seq.yaml"
      "-X": "True"
      "-P": "6"
      "-I": sample_name
    resources:
      default:
        file_size: "0"
        cores: "20"
        mem: "120000"

Why am I getting this error? How could I fix it?

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As explained in the pep docs, the sample_name column should be considered a unique identifier for a sample. The PEP requires that One row corresponds to one sample You have multiple rows with the same name; this is not allowed.

You simply need to recast your annotation sheet such that it has file1 and file2 columns, but only 2 rows.

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